Throughout the series, Heinz Doofenshmirtz was seen to have many pets, from his childhood to his adult life. Some of these pets were under his ownership for a brief moment while some of the other pets' status remain unknown.
Bobo the Rabbit is the rabbit that Heinz Doofenshmirtz used in his magic act when he was in 7th grade.
During a 7th grade magic act, Doofenshmirtz was unable to pull Bobo out of his hat, but instead accidentally pulled out a skunk. Heinz had since been searching for the rabbit, until one struggle with Perry the Platypus when the platypus used a tophat to launch it at him. ("Leave the Busting to Us!")
Mr. Fluffypants was the name Heinz Doofenshmirtz gave to a cat he found on the street. Heinz named the cat "Mr. Fluffypants" because he was fluffy and looked as if he was wearing pants. Doofenshmirtz also remarked that the cat resembled his uncle Fluffy Pants, whose name was ironic for the fact that he wore no pants.
The cat caused unrelenting havoc in Doofenshmirtz's lair, tearing up his old blueprints and reactivating his used -inators.
At the end of the day, the cat's real owner appears to reclaim his missing cat and calls him by his real name, "Mr. Cat". ("Spa Day")
Doofenshmirtz's returning the cat to his original owner can be categorized under his random acts of kindness.
He was a pet cockroach that Heinz had in his childhood back in Gimmelshtump. It was one of the few things that made him happy.
Years later, Doofenshmirtz tried to fuse a cockroach that was most likely Hoarfrost with a cone of garlic ice cream with unfavorable results. This cockroach demonstrated the ability to speak, lamenting "so cold" and saying "ow" when it was dropped on the floor. It is presumed that the roach was unfused like everything else when the molecular separator was destroyed. ("Canderemy")
The Ugly Bird was never named, although it did belong to Doofenshmirtz for at least one day (most likely stolen from an innocent child). Doofenshmirtz used it to trick Perry to walk inside his tent (its body shape and perch made it look like Doofenshmirtz's silhouette from outside the tent). It looked very much like him, who said "It's quite an ugly bird, though". ("Meatloaf Surprise").